Monkeybread is a Python package that facilitates the analysis of single-cell resolution spatial transcriptomics data such as those generated by the MERSCOPE or Xenium platforms.

Monkeybread provides tools that enable:

  • Identification of cellular niches (i.e., regions with distinct compositions of cell types)

  • Visualization of density of cell types across the tissue

  • Statistical tests for testing for colocalization between cell types

  • Statistical tests and visualiziation for ligand-receptor co-expression between neighboring cells

Monkeybread operates on datasets stored as AnnData objects and thus, can be integrated into analyses that use packages from the scverse such as scanpy or squidpy.

Monkeybread was developed at Immunitas Therapeutics.


Monkeybread requires Python 3.8 or newer installed on your system. Monkeybread can then be installed in one of two ways:

  1. Install the latest release of monkeybread from PyPI <>_:

pip install monkeybread
  1. Install the latest development version:

pip install git+

Release notes

See the [changelog][changelog].


Please use the [issue tracker][issue-tracker] to report any issues.